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- PDB-5ljn: Structure of the HOIP PUB domain bound to SPATA2 PIM peptide -

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Basic information

Entry
Database: PDB / ID: 5ljn
TitleStructure of the HOIP PUB domain bound to SPATA2 PIM peptide
Components
  • E3 ubiquitin-protein ligase RNF31
  • Spermatogenesis-associated protein 2
KeywordsLIGASE / PUB domain
Function / homology
Function and homology information


protein linear deubiquitination / protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / regulation of necroptotic process / CD40 receptor complex / negative regulation of necroptotic process ...protein linear deubiquitination / protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / regulation of necroptotic process / CD40 receptor complex / negative regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / protein K63-linked deubiquitination / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / seminiferous tubule development / ubiquitin-specific protease binding / necroptotic process / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / fibrillar center / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / signaling receptor complex adaptor activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / regulation of inflammatory response / spermatogenesis / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / ubiquitin protein ligase binding / protein-containing complex binding / zinc ion binding / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / PUB-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF31 / Spermatogenesis-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsElliott, P.R. / Komander, D.
CitationJournal: Mol.Cell / Year: 2016
Title: SPATA2 Links CYLD to LUBAC, Activates CYLD, and Controls LUBAC Signaling.
Authors: Elliott, P.R. / Leske, D. / Hrdinka, M. / Bagola, K. / Fiil, B.K. / McLaughlin, S.H. / Wagstaff, J. / Volkmar, N. / Christianson, J.C. / Kessler, B.M. / Freund, S.M. / Komander, D. / Gyrd-Hansen, M.
History
DepositionJul 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31
C: Spermatogenesis-associated protein 2
D: Spermatogenesis-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5288
Polymers41,1484
Non-polymers3804
Water00
1
A: E3 ubiquitin-protein ligase RNF31
C: Spermatogenesis-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7624
Polymers20,5742
Non-polymers1882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-15 kcal/mol
Surface area9400 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase RNF31
D: Spermatogenesis-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7664
Polymers20,5742
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-28 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.040, 89.040, 53.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin- ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 19647.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta II
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Spermatogenesis-associated protein 2 / Spermatogenesis-associated protein PD1


Mass: 926.923 Da / Num. of mol.: 2 / Fragment: UNP residues 334-341 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UM82
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.7-1.9 M (NH4)2SO4, 50 mM sodium cacodylate pH 6.4-7.0, 15 mM MgCl2 Protein:precipitant ratio; 1:2 200 nl drops
PH range: 6.4-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→62.96 Å / Num. obs: 11439 / % possible obs: 97.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 57.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.057 / Rrim(I) all: 0.098 / Net I/σ(I): 9.5 / Num. measured all: 31067
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.7-2.832.70.710.612199.7
8.96-62.962.70.0220.999190.8

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OYK

4oyk


Resolution: 2.701→62.96 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2805 627 5.49 %Random selection
Rwork0.2325 ---
obs0.2352 11425 97.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.7 Å2 / Biso mean: 61.8122 Å2 / Biso min: 29.86 Å2
Refinement stepCycle: final / Resolution: 2.701→62.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 21 0 2716
Biso mean--76.46 --
Num. residues----349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022761
X-RAY DIFFRACTIONf_angle_d0.5263758
X-RAY DIFFRACTIONf_chiral_restr0.035431
X-RAY DIFFRACTIONf_plane_restr0.004495
X-RAY DIFFRACTIONf_dihedral_angle_d16.8681667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7006-2.97230.39071610.30932745290699
2.9723-3.40240.31591430.26922709285299
3.4024-4.28650.26181630.22512681284498
4.2865-62.97790.25481600.20632663282394

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